Starting phenix.real_space_refine on Mon Mar 18 23:52:54 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dpm_27638/03_2024/8dpm_27638.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dpm_27638/03_2024/8dpm_27638.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dpm_27638/03_2024/8dpm_27638.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dpm_27638/03_2024/8dpm_27638.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dpm_27638/03_2024/8dpm_27638.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dpm_27638/03_2024/8dpm_27638.pdb" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 5526 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 69 5.16 5 C 10725 2.51 5 N 2886 2.21 5 O 3312 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "F ARG 85": "NH1" <-> "NH2" Residue "F ARG 134": "NH1" <-> "NH2" Residue "F PHE 153": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 156": "OE1" <-> "OE2" Residue "F ARG 164": "NH1" <-> "NH2" Residue "F ARG 219": "NH1" <-> "NH2" Residue "G GLU 564": "OE1" <-> "OE2" Residue "H GLU 10": "OE1" <-> "OE2" Residue "H PHE 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 156": "NH1" <-> "NH2" Residue "H TYR 174": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 187": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 209": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 50": "NH1" <-> "NH2" Residue "I ARG 59": "NH1" <-> "NH2" Residue "I ARG 67": "NH1" <-> "NH2" Residue "I ARG 104": "NH1" <-> "NH2" Residue "I ARG 114": "NH1" <-> "NH2" Residue "J TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 96": "NH1" <-> "NH2" Residue "A ARG 85": "NH1" <-> "NH2" Residue "A ARG 134": "NH1" <-> "NH2" Residue "A GLU 156": "OE1" <-> "OE2" Residue "A ARG 164": "NH1" <-> "NH2" Residue "A ARG 219": "NH1" <-> "NH2" Residue "B GLU 564": "OE1" <-> "OE2" Residue "C GLU 10": "OE1" <-> "OE2" Residue "C PHE 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 156": "NH1" <-> "NH2" Residue "C TYR 187": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 209": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 50": "NH1" <-> "NH2" Residue "D ARG 59": "NH1" <-> "NH2" Residue "D ARG 67": "NH1" <-> "NH2" Residue "D ARG 104": "NH1" <-> "NH2" Residue "D ARG 114": "NH1" <-> "NH2" Residue "E TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 96": "NH1" <-> "NH2" Residue "K ARG 85": "NH1" <-> "NH2" Residue "K ARG 134": "NH1" <-> "NH2" Residue "K PHE 153": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 156": "OE1" <-> "OE2" Residue "K ARG 164": "NH1" <-> "NH2" Residue "K ARG 219": "NH1" <-> "NH2" Residue "L GLU 564": "OE1" <-> "OE2" Residue "M GLU 10": "OE1" <-> "OE2" Residue "M PHE 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 156": "NH1" <-> "NH2" Residue "M TYR 174": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 187": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 209": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 50": "NH1" <-> "NH2" Residue "N ARG 59": "NH1" <-> "NH2" Residue "N ARG 67": "NH1" <-> "NH2" Residue "N ARG 104": "NH1" <-> "NH2" Residue "N ARG 114": "NH1" <-> "NH2" Residue "O TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 96": "NH1" <-> "NH2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 16992 Number of models: 1 Model: "" Number of chains: 21 Chain: "F" Number of atoms: 1368 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1368 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 10, 'TRANS': 166} Chain breaks: 1 Chain: "G" Number of atoms: 759 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 759 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 4, 'TRANS': 91} Chain: "H" Number of atoms: 1709 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1709 Classifications: {'peptide': 221} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 213} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "I" Number of atoms: 913 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 913 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 3, 'TRANS': 115} Chain: "J" Number of atoms: 829 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 829 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 7, 'TRANS': 102} Chain: "A" Number of atoms: 1368 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1368 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 10, 'TRANS': 166} Chain breaks: 1 Chain: "B" Number of atoms: 759 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 759 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 4, 'TRANS': 91} Chain: "C" Number of atoms: 1709 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1709 Classifications: {'peptide': 221} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 213} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "D" Number of atoms: 913 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 913 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 3, 'TRANS': 115} Chain: "E" Number of atoms: 829 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 829 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 7, 'TRANS': 102} Chain: "K" Number of atoms: 1368 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1368 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 10, 'TRANS': 166} Chain breaks: 1 Chain: "L" Number of atoms: 759 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 759 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 4, 'TRANS': 91} Chain: "M" Number of atoms: 1709 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1709 Classifications: {'peptide': 221} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 213} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "N" Number of atoms: 913 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 913 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 3, 'TRANS': 115} Chain: "O" Number of atoms: 829 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 829 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 7, 'TRANS': 102} Chain: "P" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "Q" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "R" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 72 Unusual residues: {'BMA': 1, 'MAN': 3, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "F" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "K" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 8.64, per 1000 atoms: 0.51 Number of scatterers: 16992 At special positions: 0 Unit cell: (126, 127.05, 112.35, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 69 16.00 O 3312 8.00 N 2886 7.00 C 10725 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=21, symmetry=0 Simple disulfide: pdb=" SG CYS F 108 " - pdb=" SG CYS F 135 " distance=2.03 Simple disulfide: pdb=" SG CYS F 121 " - pdb=" SG CYS F 147 " distance=2.03 Simple disulfide: pdb=" SG CYS G 511 " - pdb=" SG CYS G 556 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 161 " - pdb=" SG CYS H 226 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 98 " distance=2.03 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 90 " distance=2.03 Simple disulfide: pdb=" SG CYS A 108 " - pdb=" SG CYS A 135 " distance=2.03 Simple disulfide: pdb=" SG CYS A 121 " - pdb=" SG CYS A 147 " distance=2.03 Simple disulfide: pdb=" SG CYS B 511 " - pdb=" SG CYS B 556 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 96 " distance=2.03 Simple disulfide: pdb=" SG CYS C 161 " - pdb=" SG CYS C 226 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 98 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 90 " distance=2.03 Simple disulfide: pdb=" SG CYS K 108 " - pdb=" SG CYS K 135 " distance=2.03 Simple disulfide: pdb=" SG CYS K 121 " - pdb=" SG CYS K 147 " distance=2.03 Simple disulfide: pdb=" SG CYS L 511 " - pdb=" SG CYS L 556 " distance=2.03 Simple disulfide: pdb=" SG CYS M 22 " - pdb=" SG CYS M 96 " distance=2.03 Simple disulfide: pdb=" SG CYS M 161 " - pdb=" SG CYS M 226 " distance=2.03 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 98 " distance=2.03 Simple disulfide: pdb=" SG CYS O 22 " - pdb=" SG CYS O 90 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA P 3 " - " MAN P 6 " " MAN P 4 " - " MAN P 5 " " BMA Q 3 " - " MAN Q 6 " " MAN Q 4 " - " MAN Q 5 " " BMA R 3 " - " MAN R 6 " " MAN R 4 " - " MAN R 5 " ALPHA1-6 " BMA P 3 " - " MAN P 4 " " BMA Q 3 " - " MAN Q 4 " " BMA R 3 " - " MAN R 4 " BETA1-4 " NAG P 1 " - " NAG P 2 " " NAG P 2 " - " BMA P 3 " " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " BMA Q 3 " " NAG R 1 " - " NAG R 2 " " NAG R 2 " - " BMA R 3 " NAG-ASN " NAG A 401 " - " ASN A 228 " " NAG F 401 " - " ASN F 228 " " NAG K 401 " - " ASN K 228 " " NAG P 1 " - " ASN G 563 " " NAG Q 1 " - " ASN B 563 " " NAG R 1 " - " ASN L 563 " Time building additional restraints: 6.52 Conformation dependent library (CDL) restraints added in 2.7 seconds 4254 Ramachandran restraints generated. 2127 Oldfield, 0 Emsley, 2127 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3882 Finding SS restraints... Secondary structure from input PDB file: 15 helices and 45 sheets defined 7.7% alpha, 36.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.09 Creating SS restraints... Processing helix chain 'F' and resid 78 through 83 Processing helix chain 'G' and resid 552 through 576 removed outlier: 3.636A pdb=" N CYS G 556 " --> pdb=" O ASP G 552 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LEU G 558 " --> pdb=" O LEU G 554 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N GLN G 567 " --> pdb=" O ASN G 563 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N ALA G 568 " --> pdb=" O GLU G 564 " (cutoff:3.500A) Processing helix chain 'G' and resid 583 through 597 Processing helix chain 'I' and resid 28 through 32 Processing helix chain 'J' and resid 81 through 85 removed outlier: 3.915A pdb=" N ASP J 84 " --> pdb=" O GLN J 81 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N GLU J 85 " --> pdb=" O THR J 82 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 81 through 85' Processing helix chain 'A' and resid 78 through 83 Processing helix chain 'B' and resid 552 through 576 removed outlier: 3.644A pdb=" N CYS B 556 " --> pdb=" O ASP B 552 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LEU B 558 " --> pdb=" O LEU B 554 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ASN B 563 " --> pdb=" O ARG B 559 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N GLN B 567 " --> pdb=" O ASN B 563 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N ALA B 568 " --> pdb=" O GLU B 564 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU B 571 " --> pdb=" O GLN B 567 " (cutoff:3.500A) Processing helix chain 'B' and resid 583 through 597 Processing helix chain 'D' and resid 28 through 32 Processing helix chain 'E' and resid 81 through 85 removed outlier: 3.905A pdb=" N ASP E 84 " --> pdb=" O GLN E 81 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N GLU E 85 " --> pdb=" O THR E 82 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 81 through 85' Processing helix chain 'K' and resid 78 through 83 Processing helix chain 'L' and resid 552 through 576 removed outlier: 3.642A pdb=" N CYS L 556 " --> pdb=" O ASP L 552 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LEU L 558 " --> pdb=" O LEU L 554 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N GLN L 567 " --> pdb=" O ASN L 563 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N ALA L 568 " --> pdb=" O GLU L 564 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU L 571 " --> pdb=" O GLN L 567 " (cutoff:3.500A) Processing helix chain 'L' and resid 583 through 597 Processing helix chain 'N' and resid 28 through 32 Processing helix chain 'O' and resid 81 through 85 removed outlier: 3.915A pdb=" N ASP O 84 " --> pdb=" O GLN O 81 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N GLU O 85 " --> pdb=" O THR O 82 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 81 through 85' Processing sheet with id=AA1, first strand: chain 'F' and resid 42 through 45 removed outlier: 6.623A pdb=" N GLY F 36 " --> pdb=" O ILE F 185 " (cutoff:3.500A) removed outlier: 5.651A pdb=" N ASN F 69 " --> pdb=" O GLU F 103 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'F' and resid 42 through 45 removed outlier: 6.623A pdb=" N GLY F 36 " --> pdb=" O ILE F 185 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N VAL F 96 " --> pdb=" O THR G 581 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'F' and resid 86 through 89 Processing sheet with id=AA4, first strand: chain 'F' and resid 108 through 114 removed outlier: 6.816A pdb=" N CYS F 108 " --> pdb=" O HIS F 139 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N VAL F 141 " --> pdb=" O CYS F 108 " (cutoff:3.500A) removed outlier: 5.965A pdb=" N ASN F 110 " --> pdb=" O VAL F 141 " (cutoff:3.500A) removed outlier: 7.883A pdb=" N GLY F 143 " --> pdb=" O ASN F 110 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N GLU F 112 " --> pdb=" O GLY F 143 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N VAL F 138 " --> pdb=" O ILE F 218 " (cutoff:3.500A) removed outlier: 7.352A pdb=" N TYR F 220 " --> pdb=" O VAL F 138 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N LYS F 140 " --> pdb=" O TYR F 220 " (cutoff:3.500A) removed outlier: 7.592A pdb=" N ALA F 222 " --> pdb=" O LYS F 140 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N SER F 142 " --> pdb=" O ALA F 222 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 3 through 5 removed outlier: 3.694A pdb=" N THR H 78 " --> pdb=" O ASP H 73 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 58 through 60 removed outlier: 3.974A pdb=" N GLY H 44 " --> pdb=" O ARG H 40 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ARG H 40 " --> pdb=" O GLY H 44 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N GLU H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N MET H 34 " --> pdb=" O GLU H 50 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N TYR H 107 " --> pdb=" O ARG H 98 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 58 through 60 removed outlier: 3.974A pdb=" N GLY H 44 " --> pdb=" O ARG H 40 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ARG H 40 " --> pdb=" O GLY H 44 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N GLU H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N MET H 34 " --> pdb=" O GLU H 50 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 142 through 144 removed outlier: 3.627A pdb=" N VAL H 157 " --> pdb=" O ILE H 213 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 183 through 186 removed outlier: 6.682A pdb=" N TRP H 173 " --> pdb=" O LEU H 185 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N VAL H 223 " --> pdb=" O GLN H 176 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'I' and resid 3 through 8 Processing sheet with id=AB2, first strand: chain 'I' and resid 60 through 62 removed outlier: 6.874A pdb=" N TRP I 36 " --> pdb=" O ILE I 48 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N ARG I 50 " --> pdb=" O MET I 34 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N MET I 34 " --> pdb=" O ARG I 50 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N VAL I 37 " --> pdb=" O TYR I 97 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'I' and resid 102 through 104 Processing sheet with id=AB4, first strand: chain 'J' and resid 9 through 12 removed outlier: 6.954A pdb=" N VAL J 10 " --> pdb=" O THR J 110 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ASP J 87 " --> pdb=" O HIS J 40 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N TRP J 37 " --> pdb=" O LEU J 49 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'J' and resid 9 through 12 removed outlier: 6.954A pdb=" N VAL J 10 " --> pdb=" O THR J 110 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'J' and resid 18 through 23 Processing sheet with id=AB7, first strand: chain 'A' and resid 42 through 45 removed outlier: 6.621A pdb=" N GLY A 36 " --> pdb=" O ILE A 185 " (cutoff:3.500A) removed outlier: 5.628A pdb=" N ASN A 69 " --> pdb=" O GLU A 103 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 42 through 45 removed outlier: 6.621A pdb=" N GLY A 36 " --> pdb=" O ILE A 185 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N VAL A 96 " --> pdb=" O THR B 581 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 86 through 89 Processing sheet with id=AC1, first strand: chain 'A' and resid 108 through 114 removed outlier: 6.827A pdb=" N CYS A 108 " --> pdb=" O HIS A 139 " (cutoff:3.500A) removed outlier: 7.101A pdb=" N VAL A 141 " --> pdb=" O CYS A 108 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N ASN A 110 " --> pdb=" O VAL A 141 " (cutoff:3.500A) removed outlier: 7.881A pdb=" N GLY A 143 " --> pdb=" O ASN A 110 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N GLU A 112 " --> pdb=" O GLY A 143 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N VAL A 138 " --> pdb=" O ILE A 218 " (cutoff:3.500A) removed outlier: 7.343A pdb=" N TYR A 220 " --> pdb=" O VAL A 138 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N LYS A 140 " --> pdb=" O TYR A 220 " (cutoff:3.500A) removed outlier: 7.536A pdb=" N ALA A 222 " --> pdb=" O LYS A 140 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N SER A 142 " --> pdb=" O ALA A 222 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 3 through 5 removed outlier: 3.689A pdb=" N THR C 78 " --> pdb=" O ASP C 73 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 58 through 60 removed outlier: 3.973A pdb=" N GLY C 44 " --> pdb=" O ARG C 40 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ARG C 40 " --> pdb=" O GLY C 44 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N TRP C 36 " --> pdb=" O ILE C 48 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N GLU C 50 " --> pdb=" O MET C 34 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N MET C 34 " --> pdb=" O GLU C 50 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N TYR C 107 " --> pdb=" O ARG C 98 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 142 through 144 removed outlier: 3.636A pdb=" N VAL C 157 " --> pdb=" O ILE C 213 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 183 through 186 removed outlier: 6.676A pdb=" N TRP C 173 " --> pdb=" O LEU C 185 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N VAL C 223 " --> pdb=" O GLN C 176 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 3 through 8 Processing sheet with id=AC7, first strand: chain 'D' and resid 60 through 62 removed outlier: 6.860A pdb=" N TRP D 36 " --> pdb=" O ILE D 48 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N ARG D 50 " --> pdb=" O MET D 34 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N MET D 34 " --> pdb=" O ARG D 50 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N VAL D 37 " --> pdb=" O TYR D 97 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 102 through 104 Processing sheet with id=AC9, first strand: chain 'E' and resid 9 through 12 removed outlier: 6.951A pdb=" N VAL E 10 " --> pdb=" O THR E 110 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ASP E 87 " --> pdb=" O HIS E 40 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N TRP E 37 " --> pdb=" O LEU E 49 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'E' and resid 9 through 12 removed outlier: 6.951A pdb=" N VAL E 10 " --> pdb=" O THR E 110 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 18 through 23 Processing sheet with id=AD3, first strand: chain 'K' and resid 42 through 45 removed outlier: 6.628A pdb=" N GLY K 36 " --> pdb=" O ILE K 185 " (cutoff:3.500A) removed outlier: 5.635A pdb=" N ASN K 69 " --> pdb=" O GLU K 103 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'K' and resid 42 through 45 removed outlier: 6.628A pdb=" N GLY K 36 " --> pdb=" O ILE K 185 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N VAL K 96 " --> pdb=" O THR L 581 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'K' and resid 86 through 89 Processing sheet with id=AD6, first strand: chain 'K' and resid 108 through 109 removed outlier: 6.818A pdb=" N CYS K 108 " --> pdb=" O HIS K 139 " (cutoff:3.500A) removed outlier: 7.101A pdb=" N VAL K 141 " --> pdb=" O CYS K 108 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N GLY K 143 " --> pdb=" O GLU K 112 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'K' and resid 108 through 109 removed outlier: 6.818A pdb=" N CYS K 108 " --> pdb=" O HIS K 139 " (cutoff:3.500A) removed outlier: 7.101A pdb=" N VAL K 141 " --> pdb=" O CYS K 108 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N VAL K 138 " --> pdb=" O ILE K 218 " (cutoff:3.500A) removed outlier: 7.357A pdb=" N TYR K 220 " --> pdb=" O VAL K 138 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N LYS K 140 " --> pdb=" O TYR K 220 " (cutoff:3.500A) removed outlier: 7.574A pdb=" N ALA K 222 " --> pdb=" O LYS K 140 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N SER K 142 " --> pdb=" O ALA K 222 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'M' and resid 3 through 5 removed outlier: 3.697A pdb=" N THR M 78 " --> pdb=" O ASP M 73 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'M' and resid 58 through 60 removed outlier: 3.974A pdb=" N GLY M 44 " --> pdb=" O ARG M 40 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ARG M 40 " --> pdb=" O GLY M 44 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N TRP M 36 " --> pdb=" O ILE M 48 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N GLU M 50 " --> pdb=" O MET M 34 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N MET M 34 " --> pdb=" O GLU M 50 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N TYR M 107 " --> pdb=" O ARG M 98 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'M' and resid 58 through 60 removed outlier: 3.974A pdb=" N GLY M 44 " --> pdb=" O ARG M 40 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ARG M 40 " --> pdb=" O GLY M 44 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N TRP M 36 " --> pdb=" O ILE M 48 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N GLU M 50 " --> pdb=" O MET M 34 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N MET M 34 " --> pdb=" O GLU M 50 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'M' and resid 142 through 144 removed outlier: 3.632A pdb=" N VAL M 157 " --> pdb=" O ILE M 213 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'M' and resid 183 through 186 removed outlier: 6.684A pdb=" N TRP M 173 " --> pdb=" O LEU M 185 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N VAL M 223 " --> pdb=" O GLN M 176 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'N' and resid 3 through 8 Processing sheet with id=AE5, first strand: chain 'N' and resid 60 through 62 removed outlier: 6.867A pdb=" N TRP N 36 " --> pdb=" O ILE N 48 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N ARG N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N MET N 34 " --> pdb=" O ARG N 50 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N VAL N 37 " --> pdb=" O TYR N 97 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'N' and resid 102 through 104 Processing sheet with id=AE7, first strand: chain 'O' and resid 9 through 12 removed outlier: 6.950A pdb=" N VAL O 10 " --> pdb=" O THR O 110 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ASP O 87 " --> pdb=" O HIS O 40 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N TRP O 37 " --> pdb=" O LEU O 49 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'O' and resid 9 through 12 removed outlier: 6.950A pdb=" N VAL O 10 " --> pdb=" O THR O 110 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'O' and resid 18 through 23 556 hydrogen bonds defined for protein. 1410 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.24 Time building geometry restraints manager: 7.05 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5454 1.34 - 1.46: 4069 1.46 - 1.58: 7775 1.58 - 1.69: 0 1.69 - 1.81: 93 Bond restraints: 17391 Sorted by residual: bond pdb=" C1 MAN R 4 " pdb=" C2 MAN R 4 " ideal model delta sigma weight residual 1.526 1.565 -0.039 2.00e-02 2.50e+03 3.75e+00 bond pdb=" C1 MAN Q 4 " pdb=" C2 MAN Q 4 " ideal model delta sigma weight residual 1.526 1.565 -0.039 2.00e-02 2.50e+03 3.72e+00 bond pdb=" C1 MAN P 4 " pdb=" C2 MAN P 4 " ideal model delta sigma weight residual 1.526 1.564 -0.038 2.00e-02 2.50e+03 3.69e+00 bond pdb=" C1 MAN P 6 " pdb=" C2 MAN P 6 " ideal model delta sigma weight residual 1.526 1.561 -0.035 2.00e-02 2.50e+03 3.07e+00 bond pdb=" C1 MAN Q 6 " pdb=" C2 MAN Q 6 " ideal model delta sigma weight residual 1.526 1.560 -0.034 2.00e-02 2.50e+03 2.85e+00 ... (remaining 17386 not shown) Histogram of bond angle deviations from ideal: 100.34 - 107.07: 521 107.07 - 113.80: 9561 113.80 - 120.54: 6368 120.54 - 127.27: 6935 127.27 - 134.01: 228 Bond angle restraints: 23613 Sorted by residual: angle pdb=" CA GLY C 240 " pdb=" C GLY C 240 " pdb=" N THR C 241 " ideal model delta sigma weight residual 114.23 116.75 -2.52 8.80e-01 1.29e+00 8.20e+00 angle pdb=" C GLN G 551 " pdb=" N ASP G 552 " pdb=" CA ASP G 552 " ideal model delta sigma weight residual 121.54 126.40 -4.86 1.91e+00 2.74e-01 6.47e+00 angle pdb=" C GLN L 551 " pdb=" N ASP L 552 " pdb=" CA ASP L 552 " ideal model delta sigma weight residual 121.54 126.33 -4.79 1.91e+00 2.74e-01 6.29e+00 angle pdb=" C GLN B 551 " pdb=" N ASP B 552 " pdb=" CA ASP B 552 " ideal model delta sigma weight residual 121.54 126.28 -4.74 1.91e+00 2.74e-01 6.16e+00 angle pdb=" CA GLY C 240 " pdb=" C GLY C 240 " pdb=" O GLY C 240 " ideal model delta sigma weight residual 122.33 120.57 1.76 8.10e-01 1.52e+00 4.71e+00 ... (remaining 23608 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.43: 10148 21.43 - 42.87: 213 42.87 - 64.30: 31 64.30 - 85.74: 27 85.74 - 107.17: 12 Dihedral angle restraints: 10431 sinusoidal: 4299 harmonic: 6132 Sorted by residual: dihedral pdb=" O4 BMA Q 3 " pdb=" C4 BMA Q 3 " pdb=" C5 BMA Q 3 " pdb=" O5 BMA Q 3 " ideal model delta sinusoidal sigma weight residual -71.29 -178.46 107.17 1 3.00e+01 1.11e-03 1.38e+01 dihedral pdb=" O4 BMA R 3 " pdb=" C4 BMA R 3 " pdb=" C5 BMA R 3 " pdb=" O5 BMA R 3 " ideal model delta sinusoidal sigma weight residual -71.29 -178.44 107.15 1 3.00e+01 1.11e-03 1.38e+01 dihedral pdb=" O4 BMA P 3 " pdb=" C4 BMA P 3 " pdb=" C5 BMA P 3 " pdb=" O5 BMA P 3 " ideal model delta sinusoidal sigma weight residual -71.29 -178.41 107.12 1 3.00e+01 1.11e-03 1.38e+01 ... (remaining 10428 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.072: 2372 0.072 - 0.144: 251 0.144 - 0.216: 2 0.216 - 0.288: 3 0.288 - 0.360: 6 Chirality restraints: 2634 Sorted by residual: chirality pdb=" C1 NAG Q 1 " pdb=" ND2 ASN B 563 " pdb=" C2 NAG Q 1 " pdb=" O5 NAG Q 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.04 -0.36 2.00e-01 2.50e+01 3.25e+00 chirality pdb=" C1 NAG P 1 " pdb=" ND2 ASN G 563 " pdb=" C2 NAG P 1 " pdb=" O5 NAG P 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.06 -0.34 2.00e-01 2.50e+01 2.85e+00 chirality pdb=" C1 NAG R 1 " pdb=" ND2 ASN L 563 " pdb=" C2 NAG R 1 " pdb=" O5 NAG R 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.06 -0.34 2.00e-01 2.50e+01 2.85e+00 ... (remaining 2631 not shown) Planarity restraints: 3006 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO C 233 " -0.029 5.00e-02 4.00e+02 4.34e-02 3.01e+00 pdb=" N PRO C 234 " 0.075 5.00e-02 4.00e+02 pdb=" CA PRO C 234 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO C 234 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO M 233 " -0.028 5.00e-02 4.00e+02 4.29e-02 2.95e+00 pdb=" N PRO M 234 " 0.074 5.00e-02 4.00e+02 pdb=" CA PRO M 234 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO M 234 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO H 233 " -0.028 5.00e-02 4.00e+02 4.28e-02 2.94e+00 pdb=" N PRO H 234 " 0.074 5.00e-02 4.00e+02 pdb=" CA PRO H 234 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO H 234 " -0.024 5.00e-02 4.00e+02 ... (remaining 3003 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 2055 2.76 - 3.29: 16011 3.29 - 3.83: 28969 3.83 - 4.36: 35505 4.36 - 4.90: 62154 Nonbonded interactions: 144694 Sorted by model distance: nonbonded pdb=" OG SER F 65 " pdb=" OE1 GLU F 100 " model vdw 2.221 2.440 nonbonded pdb=" OG SER K 65 " pdb=" OE1 GLU K 100 " model vdw 2.223 2.440 nonbonded pdb=" OG SER A 65 " pdb=" OE1 GLU A 100 " model vdw 2.225 2.440 nonbonded pdb=" OD1 ASP A 117 " pdb=" OG SER A 119 " model vdw 2.270 2.440 nonbonded pdb=" OH TYR O 33 " pdb=" OD1 ASP O 99 " model vdw 2.271 2.440 ... (remaining 144689 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'F' selection = chain 'K' } ncs_group { reference = chain 'B' selection = chain 'G' selection = chain 'L' } ncs_group { reference = chain 'C' selection = chain 'H' selection = chain 'M' } ncs_group { reference = chain 'D' selection = chain 'I' selection = chain 'N' } ncs_group { reference = chain 'E' selection = chain 'J' selection = chain 'O' } ncs_group { reference = chain 'P' selection = chain 'Q' selection = chain 'R' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.820 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.130 Construct map_model_manager: 0.010 Extract box with map and model: 12.880 Check model and map are aligned: 0.230 Set scattering table: 0.130 Process input model: 45.460 Find NCS groups from input model: 1.060 Set up NCS constraints: 0.160 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 75.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7759 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 17391 Z= 0.162 Angle : 0.495 6.514 23613 Z= 0.252 Chirality : 0.044 0.360 2634 Planarity : 0.003 0.043 3000 Dihedral : 10.748 107.173 6486 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 0.62 % Allowed : 5.04 % Favored : 94.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (0.18), residues: 2127 helix: 0.01 (0.45), residues: 156 sheet: 0.19 (0.19), residues: 813 loop : 0.14 (0.18), residues: 1158 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 33 HIS 0.001 0.000 HIS A 154 PHE 0.004 0.001 PHE L 582 TYR 0.014 0.001 TYR M 187 ARG 0.002 0.000 ARG F 219 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4254 Ramachandran restraints generated. 2127 Oldfield, 0 Emsley, 2127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4254 Ramachandran restraints generated. 2127 Oldfield, 0 Emsley, 2127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 478 residues out of total 1788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 467 time to evaluate : 1.977 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 139 ASP cc_start: 0.7335 (p0) cc_final: 0.7103 (p0) REVERT: C 80 PHE cc_start: 0.7634 (OUTLIER) cc_final: 0.7188 (p90) REVERT: C 90 ASP cc_start: 0.6511 (m-30) cc_final: 0.6260 (m-30) outliers start: 11 outliers final: 3 residues processed: 476 average time/residue: 1.3173 time to fit residues: 694.6775 Evaluate side-chains 297 residues out of total 1788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 293 time to evaluate : 1.761 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 80 PHE Chi-restraints excluded: chain C residue 80 PHE Chi-restraints excluded: chain E residue 112 LEU Chi-restraints excluded: chain M residue 80 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 177 optimal weight: 8.9990 chunk 159 optimal weight: 4.9990 chunk 88 optimal weight: 2.9990 chunk 54 optimal weight: 3.9990 chunk 107 optimal weight: 5.9990 chunk 85 optimal weight: 3.9990 chunk 164 optimal weight: 0.7980 chunk 63 optimal weight: 0.3980 chunk 100 optimal weight: 5.9990 chunk 122 optimal weight: 5.9990 chunk 190 optimal weight: 6.9990 overall best weight: 2.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 39 HIS H 110 GLN H 228 GLN J 28 ASN A 39 HIS A 188 GLN B 521 GLN ** E 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 28 ASN E 55 HIS K 39 HIS K 188 GLN L 521 GLN N 103 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.2689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.050 17391 Z= 0.495 Angle : 0.699 8.521 23613 Z= 0.358 Chirality : 0.046 0.178 2634 Planarity : 0.005 0.053 3000 Dihedral : 8.038 70.325 2783 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 11.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 4.43 % Allowed : 15.52 % Favored : 80.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.19), residues: 2127 helix: 0.33 (0.41), residues: 156 sheet: 0.08 (0.18), residues: 861 loop : 0.12 (0.20), residues: 1110 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP M 36 HIS 0.006 0.001 HIS M 35 PHE 0.020 0.002 PHE D 70 TYR 0.024 0.002 TYR E 51 ARG 0.008 0.001 ARG I 114 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4254 Ramachandran restraints generated. 2127 Oldfield, 0 Emsley, 2127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4254 Ramachandran restraints generated. 2127 Oldfield, 0 Emsley, 2127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 393 residues out of total 1788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 314 time to evaluate : 2.010 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 LYS cc_start: 0.8655 (OUTLIER) cc_final: 0.8391 (mtpp) REVERT: C 80 PHE cc_start: 0.7729 (OUTLIER) cc_final: 0.7340 (p90) REVERT: C 220 ASP cc_start: 0.7728 (m-30) cc_final: 0.7480 (m-30) REVERT: K 54 ARG cc_start: 0.7316 (OUTLIER) cc_final: 0.7015 (ptm160) outliers start: 79 outliers final: 34 residues processed: 355 average time/residue: 1.3208 time to fit residues: 518.3963 Evaluate side-chains 308 residues out of total 1788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 271 time to evaluate : 2.027 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 576 THR Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 80 PHE Chi-restraints excluded: chain H residue 91 SER Chi-restraints excluded: chain H residue 106 ASP Chi-restraints excluded: chain I residue 2 VAL Chi-restraints excluded: chain I residue 5 VAL Chi-restraints excluded: chain I residue 30 SER Chi-restraints excluded: chain I residue 56 ASP Chi-restraints excluded: chain I residue 59 ARG Chi-restraints excluded: chain I residue 61 ASP Chi-restraints excluded: chain I residue 86 ASN Chi-restraints excluded: chain J residue 10 VAL Chi-restraints excluded: chain J residue 34 ASP Chi-restraints excluded: chain J residue 97 LEU Chi-restraints excluded: chain A residue 114 LYS Chi-restraints excluded: chain B residue 544 THR Chi-restraints excluded: chain C residue 4 LEU Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 80 PHE Chi-restraints excluded: chain C residue 91 SER Chi-restraints excluded: chain C residue 232 THR Chi-restraints excluded: chain D residue 61 ASP Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain E residue 10 VAL Chi-restraints excluded: chain E residue 34 ASP Chi-restraints excluded: chain K residue 54 ARG Chi-restraints excluded: chain M residue 12 VAL Chi-restraints excluded: chain M residue 20 LEU Chi-restraints excluded: chain M residue 80 PHE Chi-restraints excluded: chain M residue 91 SER Chi-restraints excluded: chain M residue 106 ASP Chi-restraints excluded: chain M residue 232 THR Chi-restraints excluded: chain N residue 2 VAL Chi-restraints excluded: chain N residue 107 THR Chi-restraints excluded: chain O residue 34 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 105 optimal weight: 4.9990 chunk 59 optimal weight: 0.0370 chunk 158 optimal weight: 0.9990 chunk 129 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 191 optimal weight: 0.9990 chunk 206 optimal weight: 4.9990 chunk 170 optimal weight: 3.9990 chunk 189 optimal weight: 2.9990 chunk 65 optimal weight: 4.9990 chunk 153 optimal weight: 0.9980 overall best weight: 1.2064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 28 ASN J 100 GLN E 28 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 moved from start: 0.2863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 17391 Z= 0.278 Angle : 0.597 8.077 23613 Z= 0.304 Chirality : 0.043 0.156 2634 Planarity : 0.004 0.048 3000 Dihedral : 7.695 65.766 2781 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 10.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 3.92 % Allowed : 17.98 % Favored : 78.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.18), residues: 2127 helix: 0.76 (0.42), residues: 156 sheet: 0.19 (0.19), residues: 759 loop : -0.12 (0.18), residues: 1212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 47 HIS 0.005 0.001 HIS M 35 PHE 0.008 0.001 PHE N 70 TYR 0.026 0.001 TYR J 51 ARG 0.010 0.001 ARG I 114 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4254 Ramachandran restraints generated. 2127 Oldfield, 0 Emsley, 2127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4254 Ramachandran restraints generated. 2127 Oldfield, 0 Emsley, 2127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 364 residues out of total 1788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 294 time to evaluate : 1.770 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 LYS cc_start: 0.8670 (OUTLIER) cc_final: 0.8189 (mtpp) REVERT: C 80 PHE cc_start: 0.7796 (OUTLIER) cc_final: 0.7307 (p90) REVERT: N 46 GLU cc_start: 0.6900 (tm-30) cc_final: 0.6538 (tm-30) outliers start: 70 outliers final: 29 residues processed: 330 average time/residue: 1.3489 time to fit residues: 493.2382 Evaluate side-chains 296 residues out of total 1788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 265 time to evaluate : 1.946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 552 ASP Chi-restraints excluded: chain G residue 576 THR Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 80 PHE Chi-restraints excluded: chain I residue 2 VAL Chi-restraints excluded: chain I residue 10 ASP Chi-restraints excluded: chain I residue 30 SER Chi-restraints excluded: chain I residue 61 ASP Chi-restraints excluded: chain J residue 34 ASP Chi-restraints excluded: chain A residue 114 LYS Chi-restraints excluded: chain B residue 519 THR Chi-restraints excluded: chain B residue 544 THR Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 80 PHE Chi-restraints excluded: chain C residue 106 ASP Chi-restraints excluded: chain C residue 232 THR Chi-restraints excluded: chain D residue 2 VAL Chi-restraints excluded: chain D residue 61 ASP Chi-restraints excluded: chain E residue 34 ASP Chi-restraints excluded: chain M residue 12 VAL Chi-restraints excluded: chain M residue 20 LEU Chi-restraints excluded: chain M residue 46 GLU Chi-restraints excluded: chain M residue 80 PHE Chi-restraints excluded: chain M residue 142 VAL Chi-restraints excluded: chain M residue 198 ASP Chi-restraints excluded: chain M residue 232 THR Chi-restraints excluded: chain N residue 28 THR Chi-restraints excluded: chain N residue 59 ARG Chi-restraints excluded: chain N residue 72 MET Chi-restraints excluded: chain N residue 102 VAL Chi-restraints excluded: chain O residue 34 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 188 optimal weight: 4.9990 chunk 143 optimal weight: 4.9990 chunk 99 optimal weight: 6.9990 chunk 21 optimal weight: 4.9990 chunk 91 optimal weight: 5.9990 chunk 128 optimal weight: 4.9990 chunk 191 optimal weight: 0.6980 chunk 202 optimal weight: 3.9990 chunk 100 optimal weight: 2.9990 chunk 181 optimal weight: 3.9990 chunk 54 optimal weight: 3.9990 overall best weight: 3.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 28 ASN E 28 ASN N 103 GLN O 28 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.3502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.058 17391 Z= 0.623 Angle : 0.729 7.978 23613 Z= 0.375 Chirality : 0.046 0.165 2634 Planarity : 0.005 0.060 3000 Dihedral : 8.064 67.381 2781 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 13.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 5.27 % Allowed : 18.15 % Favored : 76.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.45 (0.18), residues: 2127 helix: 0.74 (0.41), residues: 156 sheet: -0.33 (0.18), residues: 864 loop : -0.29 (0.19), residues: 1107 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP H 99 HIS 0.006 0.001 HIS M 35 PHE 0.012 0.002 PHE N 70 TYR 0.027 0.002 TYR E 51 ARG 0.014 0.001 ARG I 114 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4254 Ramachandran restraints generated. 2127 Oldfield, 0 Emsley, 2127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4254 Ramachandran restraints generated. 2127 Oldfield, 0 Emsley, 2127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 386 residues out of total 1788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 292 time to evaluate : 2.032 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 LYS cc_start: 0.8685 (OUTLIER) cc_final: 0.8222 (mtpp) REVERT: N 46 GLU cc_start: 0.7050 (OUTLIER) cc_final: 0.6828 (tm-30) REVERT: O 108 LYS cc_start: 0.7638 (OUTLIER) cc_final: 0.7404 (tptp) outliers start: 94 outliers final: 45 residues processed: 346 average time/residue: 1.3829 time to fit residues: 527.4993 Evaluate side-chains 315 residues out of total 1788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 267 time to evaluate : 1.848 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 552 ASP Chi-restraints excluded: chain G residue 576 THR Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 80 PHE Chi-restraints excluded: chain H residue 232 THR Chi-restraints excluded: chain I residue 2 VAL Chi-restraints excluded: chain I residue 10 ASP Chi-restraints excluded: chain I residue 30 SER Chi-restraints excluded: chain I residue 61 ASP Chi-restraints excluded: chain I residue 86 ASN Chi-restraints excluded: chain I residue 107 THR Chi-restraints excluded: chain J residue 10 VAL Chi-restraints excluded: chain J residue 28 ASN Chi-restraints excluded: chain J residue 34 ASP Chi-restraints excluded: chain J residue 102 VAL Chi-restraints excluded: chain A residue 114 LYS Chi-restraints excluded: chain B residue 519 THR Chi-restraints excluded: chain B residue 544 THR Chi-restraints excluded: chain B residue 552 ASP Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 58 THR Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 80 PHE Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 232 THR Chi-restraints excluded: chain D residue 2 VAL Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain D residue 61 ASP Chi-restraints excluded: chain D residue 72 MET Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain E residue 10 VAL Chi-restraints excluded: chain E residue 34 ASP Chi-restraints excluded: chain E residue 102 VAL Chi-restraints excluded: chain L residue 552 ASP Chi-restraints excluded: chain M residue 12 VAL Chi-restraints excluded: chain M residue 20 LEU Chi-restraints excluded: chain M residue 80 PHE Chi-restraints excluded: chain M residue 142 VAL Chi-restraints excluded: chain M residue 232 THR Chi-restraints excluded: chain N residue 28 THR Chi-restraints excluded: chain N residue 46 GLU Chi-restraints excluded: chain N residue 61 ASP Chi-restraints excluded: chain N residue 72 MET Chi-restraints excluded: chain N residue 107 THR Chi-restraints excluded: chain O residue 34 ASP Chi-restraints excluded: chain O residue 108 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 169 optimal weight: 1.9990 chunk 115 optimal weight: 0.0470 chunk 2 optimal weight: 5.9990 chunk 151 optimal weight: 0.9990 chunk 83 optimal weight: 0.6980 chunk 173 optimal weight: 5.9990 chunk 140 optimal weight: 0.6980 chunk 0 optimal weight: 1.9990 chunk 103 optimal weight: 4.9990 chunk 182 optimal weight: 0.9980 chunk 51 optimal weight: 0.7980 overall best weight: 0.6478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 516 HIS ** E 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 28 ASN O 28 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.3444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 17391 Z= 0.207 Angle : 0.622 9.632 23613 Z= 0.314 Chirality : 0.043 0.162 2634 Planarity : 0.004 0.053 3000 Dihedral : 7.311 58.891 2781 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 11.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 3.75 % Allowed : 20.56 % Favored : 75.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.18), residues: 2127 helix: 0.96 (0.41), residues: 156 sheet: -0.29 (0.18), residues: 852 loop : -0.17 (0.19), residues: 1119 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 47 HIS 0.003 0.000 HIS H 35 PHE 0.011 0.001 PHE C 148 TYR 0.028 0.001 TYR J 51 ARG 0.013 0.001 ARG D 114 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4254 Ramachandran restraints generated. 2127 Oldfield, 0 Emsley, 2127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4254 Ramachandran restraints generated. 2127 Oldfield, 0 Emsley, 2127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 354 residues out of total 1788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 287 time to evaluate : 1.643 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 68 LYS cc_start: 0.7975 (OUTLIER) cc_final: 0.7234 (tmmm) outliers start: 67 outliers final: 30 residues processed: 323 average time/residue: 1.3958 time to fit residues: 496.9612 Evaluate side-chains 296 residues out of total 1788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 265 time to evaluate : 1.721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 80 PHE Chi-restraints excluded: chain H residue 106 ASP Chi-restraints excluded: chain H residue 142 VAL Chi-restraints excluded: chain H residue 232 THR Chi-restraints excluded: chain I residue 2 VAL Chi-restraints excluded: chain I residue 61 ASP Chi-restraints excluded: chain J residue 10 VAL Chi-restraints excluded: chain J residue 28 ASN Chi-restraints excluded: chain J residue 34 ASP Chi-restraints excluded: chain J residue 68 LYS Chi-restraints excluded: chain J residue 102 VAL Chi-restraints excluded: chain B residue 544 THR Chi-restraints excluded: chain C residue 80 PHE Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 232 THR Chi-restraints excluded: chain D residue 2 VAL Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain D residue 61 ASP Chi-restraints excluded: chain D residue 95 MET Chi-restraints excluded: chain E residue 34 ASP Chi-restraints excluded: chain M residue 20 LEU Chi-restraints excluded: chain M residue 80 PHE Chi-restraints excluded: chain M residue 106 ASP Chi-restraints excluded: chain M residue 142 VAL Chi-restraints excluded: chain M residue 232 THR Chi-restraints excluded: chain N residue 28 THR Chi-restraints excluded: chain N residue 61 ASP Chi-restraints excluded: chain O residue 34 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 68 optimal weight: 0.2980 chunk 182 optimal weight: 1.9990 chunk 40 optimal weight: 0.7980 chunk 119 optimal weight: 0.0470 chunk 50 optimal weight: 9.9990 chunk 203 optimal weight: 4.9990 chunk 168 optimal weight: 2.9990 chunk 94 optimal weight: 0.8980 chunk 16 optimal weight: 0.7980 chunk 67 optimal weight: 0.6980 chunk 106 optimal weight: 3.9990 overall best weight: 0.5278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 28 ASN B 516 HIS E 28 ASN ** M 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 28 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 moved from start: 0.3483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 17391 Z= 0.193 Angle : 0.617 9.520 23613 Z= 0.311 Chirality : 0.043 0.178 2634 Planarity : 0.004 0.043 3000 Dihedral : 7.083 59.899 2781 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 11.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 3.64 % Allowed : 21.62 % Favored : 74.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.18), residues: 2127 helix: 1.14 (0.42), residues: 156 sheet: -0.13 (0.18), residues: 780 loop : -0.19 (0.19), residues: 1191 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP N 47 HIS 0.002 0.000 HIS H 35 PHE 0.010 0.001 PHE I 70 TYR 0.033 0.001 TYR O 51 ARG 0.010 0.001 ARG M 156 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4254 Ramachandran restraints generated. 2127 Oldfield, 0 Emsley, 2127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4254 Ramachandran restraints generated. 2127 Oldfield, 0 Emsley, 2127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 348 residues out of total 1788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 283 time to evaluate : 1.805 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: O 17 THR cc_start: 0.8487 (m) cc_final: 0.8018 (p) outliers start: 65 outliers final: 43 residues processed: 317 average time/residue: 1.3303 time to fit residues: 466.4242 Evaluate side-chains 309 residues out of total 1788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 266 time to evaluate : 1.847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 552 ASP Chi-restraints excluded: chain G residue 576 THR Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 80 PHE Chi-restraints excluded: chain H residue 106 ASP Chi-restraints excluded: chain H residue 142 VAL Chi-restraints excluded: chain H residue 232 THR Chi-restraints excluded: chain I residue 2 VAL Chi-restraints excluded: chain I residue 48 ILE Chi-restraints excluded: chain I residue 59 ARG Chi-restraints excluded: chain I residue 61 ASP Chi-restraints excluded: chain J residue 10 VAL Chi-restraints excluded: chain J residue 34 ASP Chi-restraints excluded: chain J residue 52 ASP Chi-restraints excluded: chain A residue 178 GLU Chi-restraints excluded: chain B residue 519 THR Chi-restraints excluded: chain B residue 544 THR Chi-restraints excluded: chain B residue 552 ASP Chi-restraints excluded: chain B residue 577 THR Chi-restraints excluded: chain C residue 80 PHE Chi-restraints excluded: chain C residue 106 ASP Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 232 THR Chi-restraints excluded: chain D residue 2 VAL Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain D residue 56 ASP Chi-restraints excluded: chain D residue 61 ASP Chi-restraints excluded: chain D residue 95 MET Chi-restraints excluded: chain E residue 34 ASP Chi-restraints excluded: chain L residue 552 ASP Chi-restraints excluded: chain L residue 566 THR Chi-restraints excluded: chain M residue 46 GLU Chi-restraints excluded: chain M residue 71 THR Chi-restraints excluded: chain M residue 80 PHE Chi-restraints excluded: chain M residue 106 ASP Chi-restraints excluded: chain M residue 142 VAL Chi-restraints excluded: chain M residue 232 THR Chi-restraints excluded: chain N residue 28 THR Chi-restraints excluded: chain N residue 61 ASP Chi-restraints excluded: chain N residue 72 MET Chi-restraints excluded: chain O residue 34 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 195 optimal weight: 7.9990 chunk 22 optimal weight: 1.9990 chunk 115 optimal weight: 6.9990 chunk 148 optimal weight: 2.9990 chunk 114 optimal weight: 4.9990 chunk 171 optimal weight: 3.9990 chunk 113 optimal weight: 0.6980 chunk 202 optimal weight: 3.9990 chunk 126 optimal weight: 4.9990 chunk 123 optimal weight: 3.9990 chunk 93 optimal weight: 1.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 28 ASN E 28 ASN O 28 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.3757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.053 17391 Z= 0.472 Angle : 0.695 8.295 23613 Z= 0.354 Chirality : 0.045 0.174 2634 Planarity : 0.005 0.080 3000 Dihedral : 7.464 59.523 2781 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 13.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 4.20 % Allowed : 21.62 % Favored : 74.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.18), residues: 2127 helix: 1.12 (0.41), residues: 156 sheet: -0.42 (0.18), residues: 843 loop : -0.25 (0.19), residues: 1128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP N 47 HIS 0.004 0.001 HIS H 35 PHE 0.014 0.001 PHE I 70 TYR 0.030 0.002 TYR J 51 ARG 0.017 0.001 ARG D 114 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4254 Ramachandran restraints generated. 2127 Oldfield, 0 Emsley, 2127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4254 Ramachandran restraints generated. 2127 Oldfield, 0 Emsley, 2127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 348 residues out of total 1788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 273 time to evaluate : 2.031 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: O 17 THR cc_start: 0.8143 (m) cc_final: 0.7871 (p) outliers start: 75 outliers final: 41 residues processed: 314 average time/residue: 1.3510 time to fit residues: 469.6248 Evaluate side-chains 304 residues out of total 1788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 263 time to evaluate : 1.837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 552 ASP Chi-restraints excluded: chain G residue 576 THR Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 80 PHE Chi-restraints excluded: chain H residue 232 THR Chi-restraints excluded: chain I residue 2 VAL Chi-restraints excluded: chain I residue 10 ASP Chi-restraints excluded: chain I residue 59 ARG Chi-restraints excluded: chain I residue 61 ASP Chi-restraints excluded: chain J residue 10 VAL Chi-restraints excluded: chain J residue 34 ASP Chi-restraints excluded: chain J residue 102 VAL Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 100 GLU Chi-restraints excluded: chain B residue 519 THR Chi-restraints excluded: chain B residue 544 THR Chi-restraints excluded: chain B residue 552 ASP Chi-restraints excluded: chain B residue 577 THR Chi-restraints excluded: chain C residue 12 VAL Chi-restraints excluded: chain C residue 80 PHE Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 232 THR Chi-restraints excluded: chain D residue 2 VAL Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain D residue 61 ASP Chi-restraints excluded: chain E residue 28 ASN Chi-restraints excluded: chain E residue 34 ASP Chi-restraints excluded: chain E residue 102 VAL Chi-restraints excluded: chain L residue 552 ASP Chi-restraints excluded: chain L residue 566 THR Chi-restraints excluded: chain M residue 46 GLU Chi-restraints excluded: chain M residue 71 THR Chi-restraints excluded: chain M residue 80 PHE Chi-restraints excluded: chain M residue 142 VAL Chi-restraints excluded: chain M residue 232 THR Chi-restraints excluded: chain N residue 10 ASP Chi-restraints excluded: chain N residue 28 THR Chi-restraints excluded: chain N residue 61 ASP Chi-restraints excluded: chain O residue 34 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 125 optimal weight: 4.9990 chunk 80 optimal weight: 0.5980 chunk 120 optimal weight: 0.6980 chunk 60 optimal weight: 8.9990 chunk 39 optimal weight: 4.9990 chunk 128 optimal weight: 0.4980 chunk 137 optimal weight: 1.9990 chunk 100 optimal weight: 0.9990 chunk 18 optimal weight: 0.8980 chunk 159 optimal weight: 0.9980 chunk 184 optimal weight: 4.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 28 ASN B 514 ASN ** E 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 28 ASN ** M 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 28 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.3754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 17391 Z= 0.224 Angle : 0.637 8.950 23613 Z= 0.322 Chirality : 0.043 0.178 2634 Planarity : 0.004 0.051 3000 Dihedral : 6.956 59.758 2781 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 12.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 3.14 % Allowed : 23.31 % Favored : 73.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.29 (0.18), residues: 2127 helix: 1.21 (0.42), residues: 156 sheet: -0.27 (0.18), residues: 786 loop : -0.23 (0.19), residues: 1185 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP N 47 HIS 0.002 0.000 HIS H 35 PHE 0.010 0.001 PHE I 70 TYR 0.029 0.001 TYR E 51 ARG 0.012 0.001 ARG I 114 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4254 Ramachandran restraints generated. 2127 Oldfield, 0 Emsley, 2127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4254 Ramachandran restraints generated. 2127 Oldfield, 0 Emsley, 2127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 1788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 283 time to evaluate : 1.913 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 184 LEU cc_start: 0.8626 (OUTLIER) cc_final: 0.8411 (pp) REVERT: I 102 VAL cc_start: 0.8853 (t) cc_final: 0.8524 (t) REVERT: E 68 LYS cc_start: 0.7981 (OUTLIER) cc_final: 0.7280 (tmmm) REVERT: O 17 THR cc_start: 0.8140 (m) cc_final: 0.7835 (p) outliers start: 56 outliers final: 32 residues processed: 316 average time/residue: 1.3060 time to fit residues: 457.3902 Evaluate side-chains 302 residues out of total 1788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 268 time to evaluate : 1.997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 184 LEU Chi-restraints excluded: chain G residue 576 THR Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 80 PHE Chi-restraints excluded: chain H residue 232 THR Chi-restraints excluded: chain I residue 2 VAL Chi-restraints excluded: chain I residue 61 ASP Chi-restraints excluded: chain J residue 34 ASP Chi-restraints excluded: chain J residue 102 VAL Chi-restraints excluded: chain B residue 519 THR Chi-restraints excluded: chain B residue 544 THR Chi-restraints excluded: chain B residue 552 ASP Chi-restraints excluded: chain B residue 577 THR Chi-restraints excluded: chain C residue 46 GLU Chi-restraints excluded: chain C residue 80 PHE Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 232 THR Chi-restraints excluded: chain D residue 2 VAL Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain D residue 61 ASP Chi-restraints excluded: chain E residue 28 ASN Chi-restraints excluded: chain E residue 34 ASP Chi-restraints excluded: chain E residue 68 LYS Chi-restraints excluded: chain L residue 566 THR Chi-restraints excluded: chain M residue 46 GLU Chi-restraints excluded: chain M residue 71 THR Chi-restraints excluded: chain M residue 80 PHE Chi-restraints excluded: chain M residue 232 THR Chi-restraints excluded: chain N residue 10 ASP Chi-restraints excluded: chain N residue 28 THR Chi-restraints excluded: chain N residue 61 ASP Chi-restraints excluded: chain O residue 34 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 193 optimal weight: 0.7980 chunk 176 optimal weight: 0.7980 chunk 188 optimal weight: 0.0270 chunk 113 optimal weight: 5.9990 chunk 82 optimal weight: 1.9990 chunk 148 optimal weight: 2.9990 chunk 57 optimal weight: 2.9990 chunk 170 optimal weight: 4.9990 chunk 178 optimal weight: 0.0270 chunk 187 optimal weight: 0.9980 chunk 123 optimal weight: 1.9990 overall best weight: 0.5296 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 28 ASN ** J 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 28 ASN M 146 HIS O 28 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.3758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 17391 Z= 0.214 Angle : 0.661 8.807 23613 Z= 0.333 Chirality : 0.043 0.173 2634 Planarity : 0.005 0.086 3000 Dihedral : 6.813 58.510 2781 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 12.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 2.52 % Allowed : 24.48 % Favored : 73.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.25 (0.18), residues: 2127 helix: 1.29 (0.42), residues: 156 sheet: -0.25 (0.18), residues: 795 loop : -0.20 (0.19), residues: 1176 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP N 47 HIS 0.003 0.001 HIS M 146 PHE 0.011 0.001 PHE I 70 TYR 0.031 0.001 TYR J 51 ARG 0.019 0.001 ARG D 67 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4254 Ramachandran restraints generated. 2127 Oldfield, 0 Emsley, 2127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4254 Ramachandran restraints generated. 2127 Oldfield, 0 Emsley, 2127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 1788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 276 time to evaluate : 1.926 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 184 LEU cc_start: 0.8632 (OUTLIER) cc_final: 0.8415 (pp) REVERT: H 80 PHE cc_start: 0.7737 (OUTLIER) cc_final: 0.7330 (m-80) REVERT: I 102 VAL cc_start: 0.8800 (t) cc_final: 0.8597 (t) REVERT: J 98 ARG cc_start: 0.7119 (mpp80) cc_final: 0.6878 (mpp80) REVERT: C 80 PHE cc_start: 0.7825 (OUTLIER) cc_final: 0.7482 (m-80) REVERT: E 68 LYS cc_start: 0.7985 (OUTLIER) cc_final: 0.7228 (tmmm) REVERT: O 17 THR cc_start: 0.8138 (m) cc_final: 0.7821 (p) outliers start: 45 outliers final: 34 residues processed: 300 average time/residue: 1.3917 time to fit residues: 465.0888 Evaluate side-chains 299 residues out of total 1788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 261 time to evaluate : 2.027 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 184 LEU Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 80 PHE Chi-restraints excluded: chain H residue 106 ASP Chi-restraints excluded: chain H residue 232 THR Chi-restraints excluded: chain I residue 2 VAL Chi-restraints excluded: chain I residue 59 ARG Chi-restraints excluded: chain I residue 61 ASP Chi-restraints excluded: chain J residue 34 ASP Chi-restraints excluded: chain J residue 102 VAL Chi-restraints excluded: chain B residue 519 THR Chi-restraints excluded: chain B residue 544 THR Chi-restraints excluded: chain B residue 552 ASP Chi-restraints excluded: chain B residue 577 THR Chi-restraints excluded: chain C residue 46 GLU Chi-restraints excluded: chain C residue 80 PHE Chi-restraints excluded: chain C residue 106 ASP Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 232 THR Chi-restraints excluded: chain D residue 2 VAL Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain D residue 61 ASP Chi-restraints excluded: chain E residue 34 ASP Chi-restraints excluded: chain E residue 68 LYS Chi-restraints excluded: chain M residue 46 GLU Chi-restraints excluded: chain M residue 71 THR Chi-restraints excluded: chain M residue 80 PHE Chi-restraints excluded: chain M residue 106 ASP Chi-restraints excluded: chain M residue 146 HIS Chi-restraints excluded: chain M residue 232 THR Chi-restraints excluded: chain N residue 2 VAL Chi-restraints excluded: chain N residue 10 ASP Chi-restraints excluded: chain N residue 28 THR Chi-restraints excluded: chain N residue 61 ASP Chi-restraints excluded: chain N residue 72 MET Chi-restraints excluded: chain O residue 34 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 199 optimal weight: 0.0000 chunk 121 optimal weight: 0.7980 chunk 94 optimal weight: 2.9990 chunk 138 optimal weight: 3.9990 chunk 209 optimal weight: 0.9980 chunk 192 optimal weight: 3.9990 chunk 166 optimal weight: 0.0970 chunk 17 optimal weight: 6.9990 chunk 128 optimal weight: 0.9980 chunk 102 optimal weight: 3.9990 chunk 132 optimal weight: 2.9990 overall best weight: 0.5782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 28 ASN ** J 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 551 GLN M 146 HIS ** N 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 28 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 moved from start: 0.3781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 17391 Z= 0.214 Angle : 0.679 10.653 23613 Z= 0.339 Chirality : 0.043 0.172 2634 Planarity : 0.005 0.085 3000 Dihedral : 6.683 57.575 2781 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 12.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 2.63 % Allowed : 24.59 % Favored : 72.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.18), residues: 2127 helix: 1.29 (0.42), residues: 156 sheet: -0.15 (0.18), residues: 759 loop : -0.29 (0.18), residues: 1212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP N 47 HIS 0.009 0.001 HIS M 146 PHE 0.009 0.001 PHE I 70 TYR 0.031 0.001 TYR E 51 ARG 0.020 0.001 ARG D 114 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4254 Ramachandran restraints generated. 2127 Oldfield, 0 Emsley, 2127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4254 Ramachandran restraints generated. 2127 Oldfield, 0 Emsley, 2127 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 1788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 275 time to evaluate : 1.941 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 184 LEU cc_start: 0.8639 (OUTLIER) cc_final: 0.8430 (pp) REVERT: H 80 PHE cc_start: 0.7768 (OUTLIER) cc_final: 0.7325 (m-80) REVERT: J 98 ARG cc_start: 0.7125 (mpp80) cc_final: 0.6877 (mpp80) REVERT: C 80 PHE cc_start: 0.7827 (OUTLIER) cc_final: 0.7459 (m-80) REVERT: E 68 LYS cc_start: 0.7958 (OUTLIER) cc_final: 0.7216 (tmmm) REVERT: O 17 THR cc_start: 0.8134 (m) cc_final: 0.7829 (p) outliers start: 47 outliers final: 33 residues processed: 300 average time/residue: 1.3617 time to fit residues: 451.6761 Evaluate side-chains 302 residues out of total 1788 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 265 time to evaluate : 1.904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 184 LEU Chi-restraints excluded: chain G residue 552 ASP Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 80 PHE Chi-restraints excluded: chain H residue 106 ASP Chi-restraints excluded: chain H residue 232 THR Chi-restraints excluded: chain I residue 59 ARG Chi-restraints excluded: chain I residue 61 ASP Chi-restraints excluded: chain J residue 34 ASP Chi-restraints excluded: chain J residue 102 VAL Chi-restraints excluded: chain B residue 519 THR Chi-restraints excluded: chain B residue 544 THR Chi-restraints excluded: chain B residue 552 ASP Chi-restraints excluded: chain B residue 577 THR Chi-restraints excluded: chain C residue 46 GLU Chi-restraints excluded: chain C residue 80 PHE Chi-restraints excluded: chain C residue 106 ASP Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 232 THR Chi-restraints excluded: chain D residue 2 VAL Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain D residue 61 ASP Chi-restraints excluded: chain E residue 34 ASP Chi-restraints excluded: chain E residue 68 LYS Chi-restraints excluded: chain L residue 552 ASP Chi-restraints excluded: chain M residue 71 THR Chi-restraints excluded: chain M residue 80 PHE Chi-restraints excluded: chain M residue 106 ASP Chi-restraints excluded: chain M residue 232 THR Chi-restraints excluded: chain N residue 2 VAL Chi-restraints excluded: chain N residue 10 ASP Chi-restraints excluded: chain N residue 28 THR Chi-restraints excluded: chain N residue 61 ASP Chi-restraints excluded: chain N residue 72 MET Chi-restraints excluded: chain O residue 34 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 177 optimal weight: 10.0000 chunk 51 optimal weight: 0.9990 chunk 153 optimal weight: 0.3980 chunk 24 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 chunk 166 optimal weight: 0.5980 chunk 69 optimal weight: 5.9990 chunk 171 optimal weight: 5.9990 chunk 21 optimal weight: 2.9990 chunk 30 optimal weight: 0.2980 chunk 146 optimal weight: 0.9990 overall best weight: 0.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 28 ASN ** J 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 28 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.077665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.058834 restraints weight = 45543.000| |-----------------------------------------------------------------------------| r_work (start): 0.3095 rms_B_bonded: 3.29 r_work: 0.2957 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.3801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 17391 Z= 0.221 Angle : 0.680 10.100 23613 Z= 0.341 Chirality : 0.043 0.175 2634 Planarity : 0.005 0.056 3000 Dihedral : 6.558 56.526 2781 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 12.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 2.69 % Allowed : 24.99 % Favored : 72.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.18), residues: 2127 helix: 1.34 (0.42), residues: 156 sheet: -0.14 (0.18), residues: 759 loop : -0.29 (0.18), residues: 1212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP N 36 HIS 0.002 0.000 HIS H 35 PHE 0.011 0.001 PHE C 148 TYR 0.032 0.001 TYR J 51 ARG 0.013 0.001 ARG D 114 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7436.52 seconds wall clock time: 132 minutes 9.04 seconds (7929.04 seconds total)